Hi,
I can understand your concern. Normally Zune software won't sync the files already sync previously, I would suggest you to try change your sync options and what will be good for you.
You can have a look at the link here below related about the files sync.
http://www.microsoft.com/windowsphone/en-us/howto/wp7/music/sync-files-with-my-phone.aspx
Thank you for your post.